From 90b02a30b410cb883c28e15885ef445cce89a63e Mon Sep 17 00:00:00 2001
From: Ziwei Huang <huang-ziwei@outlook.com>
Date: Tue, 25 Nov 2025 12:28:49 +0100
Subject: [PATCH 1/2] fix: ntype remapping yields multiple soma node

---
 skeliner/post.py   |  9 +++++++++
 tests/test_post.py | 28 ++++++++++++++++++++++++++++
 2 files changed, 37 insertions(+)

diff --git a/skeliner/post.py b/skeliner/post.py
index f17c302..1346be3 100644
--- a/skeliner/post.py
+++ b/skeliner/post.py
@@ -100,6 +100,11 @@ def _remap_ntype(
             mapped[new_idx] = ntype[old_idx]
     if new_len:
         mapped[0] = 1
+        # keep soma label unique (some remaps move old node 0 away from index 0)
+        dupes = (mapped == 1)
+        dupes[0] = False
+        if np.any(dupes):
+            mapped[dupes] = 3
     return mapped
 
 
@@ -708,6 +713,10 @@ def reroot(
 
     if set_soma_ntype and ntype is not None:
         ntype[0] = 1
+        if len(ntype) > 1:
+            dupes = (ntype == 1)
+            dupes[0] = False
+            ntype[dupes] = 3
 
     new_skel = Skeleton(
         soma=new_soma,
diff --git a/tests/test_post.py b/tests/test_post.py
index 94b3050..4b3099b 100644
--- a/tests/test_post.py
+++ b/tests/test_post.py
@@ -101,6 +101,7 @@ def test_reroot_updates_soma_and_ntype():
         s.soma.axes[0], s.radii["median"][0]
     )  # radius equals selected column
     assert s.ntype[0] == 1
+    assert int(np.sum(s.ntype == 1)) == 1
 
 
 def test_reroot_node2verts_vert2node_consistency():
@@ -125,3 +126,30 @@ def test_reroot_node2verts_vert2node_consistency():
             assert s.vert2node[v] == i
     # Soma verts now come from the new node 0's membership
     assert set(s.soma.verts.tolist()) == set(s.node2verts[0].tolist())
+
+
+def test_detect_soma_remaps_ntype_once():
+    nodes = np.array([[0, 0, 0], [0, 0, 5], [0, 5, 0]], float)
+    edges = np.array([[0, 1], [1, 2]], np.int64)
+    radii = {"median": np.array([1.0, 4.0, 1.5])}
+    skel = Skeleton(
+        soma=Soma.from_sphere(nodes[0], radii["median"][0], verts=None),
+        nodes=nodes,
+        radii=radii,
+        edges=edges,
+        ntype=np.array([1, 3, 3], np.int8),
+    )
+
+    s = post.detect_soma(
+        skel,
+        radius_key="median",
+        soma_radius_percentile_threshold=90.0,
+        soma_radius_distance_factor=4.0,
+        soma_min_nodes=1,
+        verbose=False,
+        mesh_vertices=None,
+    )
+
+    assert np.allclose(s.nodes[0], nodes[1])  # new soma promoted
+    assert s.ntype[0] == 1
+    assert int(np.sum(s.ntype == 1)) == 1

From 0d63d685598da1a150af474b3ac9e15730408551 Mon Sep 17 00:00:00 2001
From: Ziwei Huang <huang-ziwei@outlook.com>
Date: Tue, 25 Nov 2025 12:30:55 +0100
Subject: [PATCH 2/2] bump: v0.2.4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 69d8ad1..3674781 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "skeliner"
-version = "0.2.3"
+version = "0.2.4"
 description = "A lightweight neuromorphological mesh skeletonizer."
 authors = []
 requires-python = ">=3.10.0"